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qsea
•
reset
0
votes
0
replies
104
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
6 weeks ago
Researcher
• 0
0
votes
1
reply
223
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
updated 3 months ago by
Simon Pearce
• 0 • written 4 months ago by
User3088
• 0
7
votes
18
replies
3.1k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation
qsea
MEDIPS
TCGA
updated 5 months ago by
Matthias Lienhard
▴ 240 • written 7.2 years ago by
justinburgener
▴ 20
2
votes
1
reply
549
views
QSEA: normalisation >> sequencing preference
qsea
updated 16 months ago by
Matthias Lienhard
▴ 240 • written 16 months ago by
a.riediger
▴ 20
1
vote
1
reply
679
views
Manual import of CNV data (created with IchorCNA) into QSEAsest wit addCNV()
ichorCNA
qsea
updated 16 months ago by
Matthias Lienhard
▴ 240 • written 16 months ago by
a.riediger
▴ 20
1
vote
4
replies
1.2k
views
QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM
edgeR
qsea
MEDIPS
updated 21 months ago by
Simon Pearce
• 0 • written 21 months ago by
a.riediger
▴ 20
0
votes
2
replies
886
views
MBD-seq non model species
MethylSeq
ramwas
MEDIPS
qsea
updated 22 months ago by
Simon Pearce
• 0 • written 23 months ago by
Marianna
▴ 20
3
votes
8
replies
1.5k
views
Annotation using QSEA package
DNAMethylation
QSEA
MEDIP
3.0 years ago
rtrivedi1
▴ 10
7
votes
9
replies
1.7k
views
QSEA : Internal CNV analysis and cancer type-specific TCGA 450K Human Methylation Calibration Dataset
MEDIP-seq
CNV
TCGA450KHumanMethylationCalibrationDataset
qsea
PRAD
3.1 years ago
rtrivedi1
▴ 10
0
votes
1
reply
670
views
No beta scores generated in samples eluted at low salt concentration (MBD-seq) which aims to capture low methylated fragments?
qsea
updated 3.1 years ago by
Matthias Lienhard
▴ 240 • written 3.3 years ago by
el466
• 0
0
votes
1
reply
887
views
addPatternDensity in 'qsea' takes too much time
MBD-seq
qsea
BiocParallel
updated 3.5 years ago by
Matthias Lienhard
▴ 240 • written 3.5 years ago by
mbk0asis
• 0
0
votes
2
replies
798
views
Qsea - plotCoverage
Qsea
updated 4.2 years ago by
Matthias Lienhard
▴ 240 • written 4.2 years ago by
gaurav4thareja
▴ 20
1
vote
2
replies
1.0k
views
Read counts between QSEA and MEDIPs
qsea
medips
updated 4.3 years ago by
Matthias Lienhard
▴ 240 • written 4.3 years ago by
Simon Pearce
• 0
0
votes
1
reply
716
views
Qsea - addEnrichmentParameters() - Using INPUT Samples
Qsea
updated 4.3 years ago by
Matthias Lienhard
▴ 240 • written 4.3 years ago by
gaurav4thareja
▴ 20
0
votes
2
replies
1.1k
views
MBDseq analysis using qsea package
qsea
MBDseq
updated 4.8 years ago by
Matthias Lienhard
▴ 240 • written 4.9 years ago by
LNathanson
• 0
0
votes
0
replies
1.0k
views
Indexing large chromosomes (like wheat) bam files in Rsamtools
Rsamtools
QSEA
MEDIPS
5.7 years ago
saripalligautam86
▴ 10
0
votes
1
reply
893
views
Error running the addCoverage command in QSEA with a custom BSGenome reference
qsea
updated 6.0 years ago by
Matthias Lienhard
▴ 240 • written 6.1 years ago by
apt.university
• 0
0
votes
8
replies
1.6k
views
qsea non-TCGA 450K Human Methylation Calibration Dataset
qsea
updated 6.1 years ago by
Matthias Lienhard
▴ 240 • written 6.2 years ago by
wildist
• 0
0
votes
3
replies
1.2k
views
QSEA: Need help on creating ROI for whole genome MeDIPSeq data
qsea
updated 6.4 years ago by
Matthias Lienhard
▴ 240 • written 6.4 years ago by
geekyvt
• 0
1
vote
2
replies
1.0k
views
QSEA: Error while addLibraryFactors
QSEA
updated 6.4 years ago by
Matthias Lienhard
▴ 240 • written 6.4 years ago by
geekyvt
• 0
1
vote
3
replies
1.3k
views
QSEA Error while loading the bam files
qsea
updated 6.4 years ago by
Matthias Lienhard
▴ 240 • written 6.4 years ago by
geekyvt
• 0
21 results • Page
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Recent ...
Replies
Answer: Ranking the GSEA Results
by
Michael Love
42k
Some posts on this topic: https://www.google.com/search?q=site%3Asupport.bioconductor.org+GSEA+ranking+DESeq2
Answer: Advice on appropriateness of an offset in glmGamPoi/edgeR
by
Gordon Smyth
51k
edgeR allows observation specific offsets (as already pointed out), although I am not confident that would be a reliable solution to your p…
Comment: Research Project - Expanding search funtionality on the GEO database
by
gallantk5
• 0
Thank you I will take a look at those !
Comment: Research Project - Expanding search funtionality on the GEO database
by
gallantk5
• 0
I will send you an email and talk to my advisor about setting up a meeting. Thank you !
Comment: Research Project - Expanding search funtionality on the GEO database
by
Sean Davis
21k
You can use the Bioconductor Annotation packages for the Affymetrix chips of interest. - https://bioconductor.org/packages/release/BiocVie…
Votes
Answer: DESeq2 time course using fitted splines
Answer: DESeq2 time course using fitted splines
Comment: Difference between enrichGO results and Enrichr website results
Answer: Struggling to convert a large list of non-model genes into human orthologs, any
A: makeContrasts from limma overides "i" as a varible
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